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Pollen genes mutate naturally in only some strains of corn, according to Rutgers-led research that helps explain the genetic instability in certain strains and may lead to better breeding of corn and other crops.

Scientists at Rutgers University–New Brunswick and Montclair State University looked at gene mutations that arise spontaneously in corn plant pollen. Pollen grains are the male gametes, or reproductive cells, in corn plants. The scientists estimated there were several mutations per gene per million pollen grains, according to their study in the journal Proceedings of the National Academy of Sciences. The female gametes on corn ears had no detectable gene mutations.

Since a typical corn plant produces about 10 million pollen grains, a single plant in some lines, or strains, of the vital crop will produce mutations in every gene in its genome in one season. In other lines, mutations were not detected in either sex, said lead author Hugo K. Dooner, Distinguished Professor Emeritus at the Waksman Institute of Microbiology.

The United States is the world’s largest corn producer, with about 409 million tons grown on about 90 million acres in fiscal 2017-18, according to the U.S. Department of Agriculture. Feed grain consists of more than 95 percent of the production and use of corn in the United States. Corn also is processed into a wide range of food and industrial products, including cereal, alcohol, sweeteners and byproduct feeds.

In all organisms, mutations that happen spontaneously provide the raw material for natural selection and evolution. But mutations are so infrequent that scientists use special “mutation accumulation” lines to study them. The Rutgers-led team found that the mutations in pollen were caused primarily by mobile retrotransposons, which are like retroviruses in mammals, within the corn plant. Retroviruses invade cells, convert their viral RNA to DNA and merge it with the cells’ DNA.

“We found that spontaneous mutations in corn genes arise relatively frequently in the pollen of some but not all lines,” Dooner said.

Next steps are to investigate whether retrotransposon-induced mutations cause the genetic instability in corn lines previously reported by breeders, and whether activating retrotransposons in corn and other important crops could benefit them.

Rutgers co-authors include Qinghu Wang, Jun Huang, Yubin Li and Limei He at the Waksman Institute of Microbiology.

Read the paper: PNAS

Article source: Rutgers

Image: Hugo Dooner/Waksman Institute of Microbiology

Plant immune system detects bacteria through small fatty acid molecules.

Like humans and animals, plants defend themselves against pathogens with the help of their immune system. But how do they activate their cellular defenses? Researchers at the Technical University of Munich (TUM) have now discovered that receptors in plant cells identify bacteria through simple molecular building blocks.

“The immune system of plants is more sophisticated than we thought,” says Dr. Stefanie Ranf from the Chair of Phytopathology of the TU Munich. Together with an international research team, the biochemist has discovered substances that activate plant defense.

Until now, scientists have thought that plant cells – similar to those of humans and animals – recognize bacteria through complex molecular compounds, for example from the bacterial cell wall. In particular, certain molecules composed of a fat-like part and sugar molecules, lipopolysaccharides or LPS for short, were suspected of triggering an immune response.

In 2015, Ranf‘s team successfully identified the respective receptor protein: lipo-oligosaccharide-specific reduced elicitation, or LORE for short. All experiments indicated that this LORE protein activates the plant cell’s immune system when it detects LPS molecules from the cell wall of certain bacteria.

A throwback leads to the right track

“The surprise came when we wanted to study this receptor protein more closely,” recalls Ranf. “Our goal was to find out how LORE distinguishes different LPS molecules. For this we needed high-purity LPS. ”

The researchers found that only LPS samples with certain short fatty acid constituents triggered plant defense. Surprisingly, they found in all these active LPS samples also extremely strong adhering free fatty acid molecules. Only after months of experimentation was the team able to separate these free fatty acids from the LPS.

“When we finally succeeded in producing highly purified LPS, it became apparent that the plant cell did not respond to them at all! Thus, it was clear that the immune response is not triggered by LPS, but instead by these short fatty acids” said Ranf.

Targeting bacteria building blocks

The 3-hydroxy fatty acids are very simple chemical building blocks compared to the much larger LPS. They are indispensable for bacteria and are produced in large quantities for incorporation into diverse cellular components.

“The strategy of plant cells to identify bacteria through these basic building blocks is extremely sophisticated; the bacteria require these 3-hydroxy fatty acids and therefore cannot bypass the immune response,” summarizes Ranf.

Fitness program for plants

In the future, these results could help in breeding or genetically engineering plants with an improved immune response. It is also conceivable that plants treated with 3-hydroxy fatty acids would have increased resistance to pathogens.

Read the paper: Journal of Advances in Modeling Earth Systems

Article source: Science

Image: Astrid Eckert / TUM

New dynamic model better portrays how plant roots forage and adapt to resource fluctuation.

If you’ve ever tended a garden or potted a plant, you know a few simple truths about green things — they require water and nutrients to survive and their roots are good indicators of their overall health. So we water on a regular schedule, provide for root growth and add nutrient-rich soils to ensure a balanced diet.

In nature, plants don’t get that kind of care — it may not rain often enough, the earth may lack specific nutrients and there’s a lot of other vegetation vying for the same resources. While leaves and branches reach skyward to capture the sun’s energy, the roots are hard at work, scrounging for those vital water and nutrient sources.

“If a plant can adjust to environmental changes by increasing its access to resources, then it has a higher chance to survive or, more importantly, to thrive.” — Says Beth Drewniak, Argonne assistant climate scientist.

Environmental scientists have long used computer models to understand this root-to-resource dynamic, but until recently, these simplified models employed a fixed system of roots that doesn’t account for variations in resource stratification or, for that matter, the active foraging and adaption skills of roots.

A new root algorithm developed by Beth Drewniak, an assistant climate scientist with the U.S. Department of Energy’s (DOE) Argonne National Laboratory, is among the first to shed more light on the ability of plants to adapt to local changes in environment.

In a paper published in the Journal of Advances in Modeling Earth Systems, Drewniak describes a dynamic root model that she introduced into the Energy Exascale Earth System Land Model (ELM), a component of the DOE’s larger Energy Exascale Earth System Model (E3SM).

“The fixed approach has been popular in models because roots are hard to observe and study, making them difficult to understand,” says Drewniak. ​“By adding a dynamic root model component, the simulation of vegetation growth can respond to changes in resources, increasing availability of those needed resources.”

The model examines roots for all vegetation in ELM — trees, shrubs, grasses and crops — across many ecosystems and over different seasons. Where previous attempts at dynamic root models focused on either maximizing water uptake or nitrogen uptake, Drewniak’s addresses both.

“Ecosystems need to respond to many types of stress, including short- or long-term events like drought or nutrient loading,” says Drewniak. ​“If a plant can adjust to environmental changes by increasing its access to resources, then it has a higher chance to survive or, more importantly, to thrive.”

For example, changes in regional climate could result in less precipitation or shifts in the frequency of precipitation, she notes. The dynamic root model simulates how plants can acclimate to the new distribution of water in the soil by allocating roots to those layers with higher water content.

The new root distribution within the model is driven by water stress — how much water a plant needs versus how much water is available. When water stress is high, the plant focuses root growth where water is present in the soil. When the plant has ample water, root growth is concentrated where nitrogen exists. Changes to root distribution, notes Drewniak, affect a plant’s water uptake, which can impact evapotranspiration, photosynthesis, productivity, and other plant dynamics.

To gauge the model’s accuracy, Drewniak focused on how well the model performed compared with observations of root distribution and vegetation growth, as well as the model’s sensitivity to water stress. Overall, the dynamic root model was able to capture the vertical distribution of roots fairly well and improved the simulated productivity of vegetation compared with satellite observations.

Regions in which the model does not fare well include the Amazon, African tropics and southern Asia during their dry seasons, when plants typically rely on deep roots to extract water, which is not captured well by ELM.

While the dynamic root model has already made small but important improvements to ELM, it has the potential to allow it to model a more dynamic plant root response to extreme events, such as drought, that can have a big impact on the carbon and water cycle.

“The biggest lesson learned in this study is that there is more work to be done,” says Drewniak. ​“The model is improved because vegetation can respond to changes in the environment by foraging for water and nitrogen. But the study also revealed that there are other model development pieces necessary to fully capture vegetation response.”

Read the paper: Journal of Advances in Modeling Earth Systems

Article source: Argonne National Laboratory

Image: Roser Matamala, Argonne National Laboratory

Maize is a staple crop that came from humble beginnings. If you look at its wild ancestor, teosinte, the plant looks nearly unrecognizable. Human selection has persuaded the maize plant to grow in a way that produces higher yields and can be more efficiently harvested. But scientists and farmers are looking for ways, in the face of climate change, population growth, and other factors, to even further optimize maize yields.

Now, researchers at Cold Spring Harbor Laboratory (CSHL) have identified a relationship between crop yield in the maize plant and specific genetic activity associated with one of the plant’s metabolic pathways. The discovery has implications for plant breeding, potentially opening the door for increasingly resilient, higher-yield maize plants.

CSHL Professor David Jackson and his team have connected the RAMOSA3 gene to branching, which can affect its yield. When a maize plant has too many branches, it will expend more energy towards making those branches, and less towards making seeds. More branches often means lower or less efficient yields.

Ears, the part of maize that we eat, are normally not branched at all—they just form one straight cob. But maize mutants that don’t have the RAMOSA3 gene can end up with gnarly-looking branched ears.

Jackson and his team initially hypothesized that the enzyme that RAMOSA3 encodes, called TPP, and a sugar phosphate called T6P which TPP acts on, are likely responsible for the ear-branching. Although the precise function of T6P remains “largely elusive,” the scientists believe that it has signaling properties.

Then, in a surprising twist, they found that a related gene, TPP4, also helps to control branching, but that gene’s effect was unrelated to its enzymatic activity. They wondered if the same might be true for RAMOSA3 and its own enzymatic activity. To follow up on this, they blocked only the enzyme activity associated with RAMOSA3, and not the gene itself, and got normal-looking ears of maize. This indicates that although RAMOSA3 controls the activity of the enzyme, it seems the enzyme activity is not responsible for controlling branching. Thus, the gene may be “moonlighting” with a hidden activity, explains Jackson. The question of what that moonlighting may entail is a launching-off point for future research.

The team’s findings were published in Nature Plants. Their work could lead to better crop yields and more efficient harvesting for the maize plant, as well as for other crops, like rice and quinoa.

Read the paper: Nature Plants

Article source: Cold Spring Harbor Laboratory

Image: Cold Spring Harbor Laboratory

CABI has led an international team of Non-Native Species (NNS) specialists who have compiled a list of recommendations to improve the way in which the impact of a range of invasive pests – such as the tomato leaf miner Tuta absoluta – are assessed, potentially helping towards ensuring greater global food security.

Lead authors Dr Pablo González-Moreno and Dr Marc Kenis, Senior Researchers at CABI are two of 89 NNS experts from around the world who have collaborated on the paper, published in NeoBiota, that calls for ‘more robust and user-friendly’ impact assessment protocols to predict the impacts of new or likely invaders as well as to assess the actual impact of established species.

The manuscript is the outcome of an enormous collective effort using 11 different protocols to assess the potential impact of 57 NNS to Europe yielding a total of 2614 separate assessments. This unique dataset has allowed the authors to identify which are the main factors increasing the robustness of protocols and provide recommendations on how the robustness and applicability of protocols could be enhanced for assessing NNS impacts.

As reported in the study, entitled ‘Consistency of impact assessment protocols for Non-Native Species’, Dr González-Moreno and fellow scientists – from 80 institutions including the UK-based Centre for Ecology & Hydrology (CEH), University of Milan, University of Bern and Queens University Belfast – argue that ‘assessment of the realised or potential impacts of NNS is particularly important for the prioritization of management actions.’

Millions of the world’s most vulnerable people face problems with invasive weeds, insects and plant diseases, which are out of control and have a major impact on global prosperity, communities and the environment. Developing countries are disproportionately affected.

The global cost of the world’s 1.2 million invasive species is estimated at $1.4 trillion per year – close to 5 percent of global gross domestic product. In East Africa, five major invasive species alone cause $1 billion in economic losses to smallholder farmers each year.

The scientists believe that, currently, the large variety of metrics adopted to measure the impacts of invasive species undermines direct comparison of impacts across species, groups of taxa, localities or regions. They go on to argue that in general we have ‘little understanding of the patterns in consistency of impact scores across assessors and protocols, and more importantly, which factors contribute to high levels of consistency.’

Dr González-Moreno said, “There is an increasing demand for robust and user-friendly impact assessment protocols to be used by professionals with different levels of expertise and knowledge.

“Robust NNS impact protocols should ideally result in accurate and consistent impact scores for a species even if applied by different assessors, as long as they have the adequate expertise in the assessed species and context.

“Several key factors should be taken into account when selecting or designing an NNS risk assessment protocol, such as the aim, the scope, the consistency and the accuracy of the outcomes, and the resources available to perform the assessment – for example time or information available.”

In compiling a list of recommendations for improved NNS impact protocols, Dr González-Moreno and the team of researchers used 11 different protocols to assess the potential impact of 57 species not native to Europe and belonging to a very large array of taxonomic groups (plants, animals, pathogens) from terrestrial to freshwater and marine environments.

They agree that using a ‘5-level scoring, maximum aggregation method and the moderation of expertise requirements’ offers a good compromise to reducing inconsistencies in research findings without losing discriminatory power or usability.

Dr González-Moreno added, “In general, we also advise protocol developers to perform sensibility tests of consistency before final release or adoption. This is crucial as if a protocol yields inconsistent outcomes when used by different assessors, then it is likely that decisions taken based on the results could be variable and disproportionate to the actual impacts.”

Read the paper: NeoBiota

Article source: CABI

Image: CCO Public domain

If you’ve ever dined on the tropical island of Okinawa, Japan, your plate may have been graced by a remarkable pile of seaweed, each strand adorned with tiny green bubbles. Known as umi-budo or sea grapes, the salty snack pairs well with rice, sashimi and a tall glass of beer. But umi-budo is more than an iconic side dish; it’s a staple crop for Okinawan farmers. Researchers at the Okinawa Institute of Science and Technology Graduate University (OIST) recently decoded the sea grape genome to learn about the plant’s unique morphology and assist farmers in proper cultivation of the succulent seaweed.

“Many farmers face problems with sea grapes growing poorly. Today, they don’t know why such problems occur,” said Dr. Asuka Arimoto, first author of the study and a postdoctoral scholar in the OIST Marine Genomics Unit, led by Prof. Noriyuki Satoh. “Our genomic data can show them which genes are causing such trouble.” With a catalog of all the genes controlling sea grape growth, said Arimoto, the researchers may be able to help farmers diagnose deficient plants when they crop up. The research could also help curb the spread of closely-related green seaweeds, which harm the environment by pushing out local plant varieties in the Mediterranean Sea and Pan-Pacific.

The study, in DNA Research, utilized sample sea grapes from the Onna Village Fishery Cooperative, whose greenhouses are located just around the corner from OIST campus. The scientists deciphered the full sea grape genome and compared it to 15 published plant genomes, collected from unicellular algae, a type of moss, rice and thale cress. The research revealed key genes that allow sea grapes, a unicellular organism, to don its complex shape, and demonstrated the utility of using the algae to explore evolutionary processes in green plants.

“Recently, other countries have started cultivating this and related species of green seaweed,” said Arimoto. “I think this genomic information could help their future development, as well as Okinawa prefecture.”

Collection of Genes Creates “Puchi Puchi”

Tiny green balls branch off the central stem of the umi-budo plant, and when chewed, these teeny orbs burst in a pop of salty goodness. In Japanese, this sensational texture is known as “puchi puchi,” an onomatopoeia mimicking the sound of puny pops. The Marine Genomics Unit was curious as to how a plant made up of just one cell could grow into such a fantastical shape, thus granting sea grapes their singular texture.

“When we started the project, there were no [decoded] green seaweed genomes,” said Arimoto. “It was completely unknown how many genes are present in green seaweed, and which plant hormones are present to drive development.” The researchers succeeded in deciphering a high-quality genome from an umi-budo plant and compared it to known plant genomes to see whether certain genes appeared in different quantities between them.

The results suggest that the sea grapes contain an expanded set of genes thought to be descended from a core gene set found in a common ancestor of green plants. Among these genes are those that code for nuclear transport regulators—proteins that help control how information moves between the nuclei and the cytosol, the liquid in which a cell’s organelles float. In multicellular organisms, transport regulators tune whole cells to only receive certain signals, like a dial on a radio. In umi-budo, a unicellular organism, the proteins do the same for individual nuclei in the cell.

The mechanism allows single cells to take on complex shapes despite lacking cell membranes to separate one region from the next. Without nuclear transport regulators, sea grapes couldn’t grow in their signature clusters.

Compared to other green algae, sea grapes also have extra genes to code for homeobox proteins, which help to regulate the physical development of plants. Homeobox proteins flip switches on critical genes to turn them “on” or “off,” said Arimoto, which triggers cellular processes and shapes an organism’s anatomical structure down the line.

Helping Sea Grape Farmers in Okinawa and Beyond

In the future, the Marine Genomics Unit hopes to analyze gene expression as it occurs throughout the sea grape life cycle. For instance, evidence suggests that specific homeobox genes are highly expressed in the pollens and eggs of land plants. They may hold similar importance in the early life stages of umi-budo. As sea grape cultivation takes root beyond Okinawa and across the Pacific, this genomic data could help farmers establish more effective growing strategies.

While OIST researchers work with umi-budo in the lab, food-lovers can continue to order the delectable seaweed in restaurants across Japan, likely topped with a light dressing of vinegar, mirin and soy sauce. Oishi!

Read the paper: DNA Research

Article source: Okinawa Institute of Science and Technology Graduate University (OIST)

Image: Ken Maeda (OIST)

Duckweeds – for many aquatic animals like ducks and snails, a treat, but for pond owners, sometimes a thorn in the side. The tiny and fast-growing plants are of great interest to researchers, and not at least because of their industrial applications – for example, to purify wastewater or generate energy. An international research team from Münster, Jena (both Germany), Zurich (Switzerland) and Kerala (India) have recently studied the genomics of the giant duckweed. They discovered that genetic diversity, i.e. the total number of genetic characteristics that are different among individuals, is very low. “This is remarkable given that their population size is very large – there can, for example, be millions of individuals in a single pond”, says Shuqing Xu, professor for plant evolutionary ecology at the University of Münster and lead author of the study.

To understand the reason behind this mystery, a team of plant researchers headed by Dr. Meret Huber from the Max Planck Institute for Chemical Ecology in Jena and the University of Münster measured the mutation rate of this duckweed under outdoor conditions, i.e. how many mutations accumulate per generation. The result: low genetic diversity in this plant was accompanied by an extremely low mutation rate. “Our study emphasizes that accurate estimates of mutation rates are important for explaining patterns of genetic diversity among species”, says Meret Huber. The results are not only relevant for future studies on the evolution of plants, including many crops that have similar reproductive strategies like duckweeds, they will also accelerate the use of duckweeds both for basic research and industrial applications. The study was published in the journal “Nature Communication”.

Background

Although mutations are the raw materials for evolutionary changes, they are often accompanied by fitness impairments. Evolutionary researchers have hypothesized that natural selection in species with large populations drives the mutation rate to as low as possible. According to this hypothesis, a species with a very large population size may under certain conditions evolve an extremely low mutation rate – which in turn can result in a very low genetic diversity. Until now, however, scientists had not been able to show this connection in eukaryotes, i.e. organisms whose cells have a nucleus. One reason for this is that mutation rates are difficult to measure experimentally.

The researchers took samples of the giant duckweed (Spirodela polyrhiza) from 68 waterbodies distributed all over the world and read the DNA sequences of their entire genomes. They found that in congruence with their geographic origin the samples fall into four genetic clusters: America, Europe, India and Southeast Asia. Based on the genome sequence information, they found that the genetic diversity of the species is among the lowest values reported in multicellular eukaryotes.

Because genetic diversity is determined by mutation rate and effective population size, the scientists then experimentally estimated the mutation rates and calculated effective population size. Since external conditions can influence the mutation rate, they performed the experiments under outdoor conditions. The result: by sequencing genomes, they found that the mutation rate in the giant duckweed was the lowest ever determined for multicellular eukaryotes. The estimated effective population size, as expected, is rather large.

The researchers suspect that the enormous population size of the giant duckweed, and therefore the large possibilities of selection in the course of evolution, has led to the reduction of mutations to a minimum. This in turn can explain the low genetic diversity. “Our study provides new insights into why and how genetic diversity differs among different species”, says Shuqing Xu.

Together with their collaborators, the scientists are currently working on analyzing genomes of even more duckweed samples and plan to carry out outdoor selection experiments. They wish to discover which other factors might have played roles in shaping the evolution of this plant.

Read the paper: Nature Communication

Article source: University of Münster

Image: Close-up of the giant duckweed. Credit: Klaus J. Appenroth